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- PDB-5yl0: The crystal structure of Penaeus vannamei nodavirus P-domain (P212121) -

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Basic information

Entry
Database: PDB / ID: 5yl0
TitleThe crystal structure of Penaeus vannamei nodavirus P-domain (P212121)
ComponentsCapsid protein
KeywordsVIRAL PROTEIN / viral capsid protein
Function / homologyIcosahedral viral capsid protein, S domain / Viral coat protein (S domain) / T=3 icosahedral viral capsid / Viral coat protein subunit / structural molecule activity / metal ion binding / Capsid protein
Function and homology information
Biological speciesPenaeus vannamei nodavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 Å
AuthorsChen, N.C. / Yoshimura, M. / Lin, C.C. / Guan, H.H. / Chuankhayan, P. / Chen, C.J.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology105-2311-B-213-001-MY3 Taiwan
CitationJournal: Commun Biol / Year: 2019
Title: The atomic structures of shrimp nodaviruses reveal new dimeric spike structures and particle polymorphism.
Authors: Nai-Chi Chen / Masato Yoshimura / Naoyuki Miyazaki / Hong-Hsiang Guan / Phimonphan Chuankhayan / Chien-Chih Lin / Shao-Kang Chen / Pei-Ju Lin / Yen-Chieh Huang / Kenji Iwasaki / Atsushi ...Authors: Nai-Chi Chen / Masato Yoshimura / Naoyuki Miyazaki / Hong-Hsiang Guan / Phimonphan Chuankhayan / Chien-Chih Lin / Shao-Kang Chen / Pei-Ju Lin / Yen-Chieh Huang / Kenji Iwasaki / Atsushi Nakagawa / Sunney I Chan / Chun-Jung Chen /
Abstract: Shrimp nodaviruses, including (PvNV) and nodaviruses (MrNV), cause white-tail disease in shrimps, with high mortality. The viral capsid structure determines viral assembly and host specificity ...Shrimp nodaviruses, including (PvNV) and nodaviruses (MrNV), cause white-tail disease in shrimps, with high mortality. The viral capsid structure determines viral assembly and host specificity during infections. Here, we show cryo-EM structures of  = 3 and  = 1 PvNV-like particles (PvNV-LPs), crystal structures of the protrusion-domains (P-domains) of PvNV and MrNV, and the crystal structure of the ∆N-ARM-PvNV shell-domain (S-domain) in  = 1 subviral particles. The capsid protein of PvNV reveals five domains: the P-domain with a new jelly-roll structure forming cuboid-like spikes; the jelly-roll S-domain with two calcium ions; the linker between the S- and P-domains exhibiting new cross and parallel conformations; the N-arm interacting with nucleotides organized along icosahedral two-fold axes; and a disordered region comprising the basic -terminal arginine-rich motif (N-ARM) interacting with RNA. The N-ARM controls  = 3 and  = 1 assemblies. Increasing the /-termini flexibility leads to particle polymorphism. Linker flexibility may influence the dimeric-spike arrangement.
History
DepositionOct 16, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.2Feb 27, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Mar 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.4Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsid protein
B: Capsid protein
C: Capsid protein
D: Capsid protein


Theoretical massNumber of molelcules
Total (without water)50,2324
Polymers50,2324
Non-polymers00
Water26,5901476
1
A: Capsid protein
B: Capsid protein


Theoretical massNumber of molelcules
Total (without water)25,1162
Polymers25,1162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-14 kcal/mol
Surface area9890 Å2
MethodPISA
2
C: Capsid protein
D: Capsid protein


Theoretical massNumber of molelcules
Total (without water)25,1162
Polymers25,1162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-15 kcal/mol
Surface area9840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.843, 69.736, 146.606
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Capsid protein


Mass: 12558.083 Da / Num. of mol.: 4 / Fragment: UNP residues 250-368
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penaeus vannamei nodavirus / Production host: Escherichia coli (E. coli) / References: UniProt: A5H7Q8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1476 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.075M Magnesium chloride hexahydrate, 0.1M Sodium cacodylate 6.5, 30%(w/v) PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Apr 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.22→30 Å / Num. obs: 134587 / % possible obs: 86.9 % / Redundancy: 4.5 % / Rpim(I) all: 0.059 / Rrim(I) all: 0.128 / Rsym value: 0.112 / Net I/σ(I): 38.6
Reflection shellRedundancy: 4.8 % / CC1/2: 0.856 / Rpim(I) all: 0.214 / Rrim(I) all: 0.49 / Rsym value: 0.438 / % possible all: 86.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.22→23.26 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.936 / SU B: 0.666 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.06 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22039 5861 5 %RANDOM
Rwork0.17465 ---
obs0.17695 110940 87.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.942 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20 Å2
2--0.05 Å2-0 Å2
3---0.14 Å2
Refinement stepCycle: 1 / Resolution: 1.22→23.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3321 0 0 1477 4798
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.023373
X-RAY DIFFRACTIONr_bond_other_d0.0020.023262
X-RAY DIFFRACTIONr_angle_refined_deg2.1371.9664603
X-RAY DIFFRACTIONr_angle_other_deg1.01537540
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1095442
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.34926.174115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.02315554
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.128154
X-RAY DIFFRACTIONr_chiral_restr0.1490.2593
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213758
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02674
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3121.2621780
X-RAY DIFFRACTIONr_mcbond_other1.3031.2611779
X-RAY DIFFRACTIONr_mcangle_it1.7771.92218
X-RAY DIFFRACTIONr_mcangle_other1.7811.9012219
X-RAY DIFFRACTIONr_scbond_it2.5741.5251593
X-RAY DIFFRACTIONr_scbond_other2.5741.5261594
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8192.1882386
X-RAY DIFFRACTIONr_long_range_B_refined17.28419.3416542
X-RAY DIFFRACTIONr_long_range_B_other17.76515.1794997
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.221→1.253 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 428 -
Rwork0.222 8284 -
obs--88.86 %

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